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for OBD2 you still need your factory ECU connected to the diagnostics port. when they do the check, they plug into the diag port and read codes. the ECU has to tell the inspection computer that it has certain 'ready flags' set to true, and no stored codes. you cant just rig some EMS up that controls the check engine light to turn on and such...
BUT you can prob get away with this if you live in a place that only tests 97 and up OBD2 this way.. around me they used to do a tail pipe test for older cars, now it is just visual, and new cars do the plug in diagnostics. I gave up on my piggy back subaru that could not be reflashed as I could not get much more power out of it without resorting to methods thaty would not keep it 100% emisisons legal. I used an emange piggy back and a rising rate regulator in order to get enough fuel to double whp. I could not go to larger injectors as the ecu + piggy back would keep throwing CEL for too low MAP signal at low loads, therefore failing the plug in computer check.
Now the nemesis is configured for some cars in parallel with the ECU to allow the factory ecu to do stuff liek the CAN bus, evap emissions, and drive by wire etc. This might be adequate to keep the factory ecu sending the all good to the diag port, probably provided the engine is operating within parameters that make it happy.
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